Align Basic membrane lipoprotein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate WP_097028706.1 CRO07_RS00330 BMP family ABC transporter substrate-binding protein
Query= TCDB::D2BKA1 (350 letters) >NCBI__GCF_900207575.1:WP_097028706.1 Length = 331 Score = 147 bits (371), Expect = 4e-40 Identities = 109/341 (31%), Positives = 160/341 (46%), Gaps = 36/341 (10%) Query: 16 VAVLAGCRSHDAAGSGKAKTDLKAAIVTDTGGVNDRSFNQSAWEGLQSWGKENNLKKGTG 75 + LAG + A + A D A++ D GG D+SFN++A+ G Q W +E G Sbjct: 4 IRTLAGSAAAFALSAAGALAD--PALIFDLGGKFDKSFNEAAYNGAQRWVQET----GGS 57 Query: 76 YTYFQSNSASDYTTNYNSAEQQGYKLLFGIGFSLQDATSAAAKNNPKSNFVIVDSVIKDQ 135 Y + S + + G + GF+ D + A + P + F I+D+V+ +Q Sbjct: 58 YKELEMQSEAQREQALRRLAETGANPIVMTGFAFGDVLNEVAPDYPDTRFAIIDAVV-EQ 116 Query: 136 KNVASATFADNESAYLAGVAAAKATKTNKIGFIGGMQSDVITRFEKGYEAGAKSVNPDIK 195 NV S F++++ +YL G+ AA A+K+ +GF+GGM +I +F GY G K+V PD Sbjct: 117 PNVRSVIFSEHQGSYLVGMMAAMASKSGTVGFVGGMDIPLIRKFACGYAQGVKAVKPDAT 176 Query: 196 VDVQYAG----SFSDAAKGKTIAAAMYGAGDDVVYQCAGGVGTGVFSEAKALNSTKNEAD 251 V + G +++D KG +A + G DV+Y AG G GV A N Sbjct: 177 VVINMTGTTPAAWADPVKGAELARSQISQGADVIYAAAGSTGLGVLQAAADEN------- 229 Query: 252 KVWVIGVDQDQEYLGKYKSKDGKDSNFVLVSTIKEVGNVVKDIADKTKDGKFPGGTIVTY 311 + IGVD +Q +L K VL S IK V V D GT++ Sbjct: 230 -ILSIGVDSNQNHLHPGK---------VLTSMIKRVDIAVHDAF--AAGAAIETGTVLA- 276 Query: 312 DLKNGGVNLGLDSAN-----SEIKDAVAKAKADIIDGKITV 347 DLK GV LD N +E+K AV +A A I G+ V Sbjct: 277 DLKGDGVGYALDEHNAALVTAEMKAAVDEAAARIKSGETPV 317 Lambda K H 0.310 0.128 0.353 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 291 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 350 Length of database: 331 Length adjustment: 28 Effective length of query: 322 Effective length of database: 303 Effective search space: 97566 Effective search space used: 97566 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory